Thanks for the suggestions. I'll upload some photos later tonight. I took some yesterday, but the quality is too bad to be useful.
So far I checked:
r1 and r2 are not shorted,
All LEDs are the correct orientation with the anodes going to the holes marked with the circles. In testing then I found that the LEDs on SW14 to SW18 the LEDs passed voltage (approx 1.6v) in both directions, I'm guessing this isn't as it should be?
I also found my Multimeter does not light any of the LEDs in diode test mode except the red 'recording' one. Maybe it doesn't put out enough power for the clear ones?
The Cathodes are shorted in pairs to the switch below eg. SW9 is connected to SW14. I guess this is by design and not an issue?
I'll do the tests with NG firmware tonight as well, but when I originally tested all button functions were OK (no latching, registering on and off as separate events) but the problem LEDs were still stuck on.

Thought I'd report back, the above issues are solved. They were soldering issues, some really stupid some harder to find.
I still have an issue I'd like to fix, the stop, rewind, fast forward and pause buttons are constantly lit up. They function correctly when pushed, but I'm assuming this is not normal?

Ugh, I seem to have problems at every stage :(
So I have gotten to the Fluxtest and have issues on both boards.
On the LH board, no red led on SW14. Have tested the LED with multimeter and it's fine.
On the RH board, no green or blue on SW7 and SW15, same as above, LEDs are OK.
I've tried the usual, looking for obvious faults, diodes are all correct., soldering all looks OK. Any hints on where to look?

Hi, I am loading seq_l and have both boards connected as in the video, setting debug to on.
It is the left Lemec board that I am having trouble with. All other encoders/switches register except SW17-20.

After a couple of weeks break from the build, I'm back. I tried soldering in the MEC switches that are where the bridge is on both boards. Still no response from SW17-20.....Any other hints where I should look?
I've also noticed some of the LEDs on the JA PCB light up now when running the seq_l code.(SW14-18 light up).

I use two kinds, both Kester brand. Both are leaded, one with a water clean flux and the other a no clean flux. I find the water clean solder flows much more reliably, but I was worried about the Super LEDs getting wet seeing as there is a warning about humidity exposure on the video.
Also the no-clean solder leaves most of the joints looking dull like a cold joint, so this is annoying when it comes to diagnosing. Which is why I am reflowing things here and there without any real plan.

I have SW9-12 working now. But still no SW17-20 (on both LEMEC boards). All diodes are correct. Transistors too.
Do I need to solder in the MEC switches? In the build video they are not soldered in and the testing works.